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The Largest Plastid Genome of Monocots: a Novel Genome Type Containing AT Residue Repeats in the Slipper Orchid Cypripedium japonicum

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Abstract

Plastid genome studies on Orchidaceae, one of the largest families of flowering plants, have been limited to the subfamily Epidendroideae. To increase understanding of the plastid genome evolution in Orchidaceae, we performed a complete plastid genome analysis of the slipper orchid Cypripedium japonicum positioned in the basal clade of the family. No significant gene deletions were observed in the plastid genome of the slipper orchid composed of 85 coding genes including members of the ndh gene family, which are mostly deleted or show pseudogenisation in orchids, although matK was identified as a pseudogene due to a frameshift mutation. Results also revealed that C. japonicum contains the largest plastid genome (174,417 bp) within monocots and the third largest one in Magnoliophyta. This is a new type of plastid genome extended due to abnormally frequent AT residue repeats within noncoding regions without inverted repeat (IR) expansion. In addition, we detected 25 plastid microsatellites and compared them among seven populations from Korea and Japan. These microsatellites may be applicable to population genetics and conservation biology studies on slipper orchids, which have become rare and are nearing extinction. AT-rich regions in the introns may also play a role in effective splicing of the genome after matK lost its function. As AT-rich regions are difficult to amplify and sequence using normal sequencing technologies, we propose a revised methodology for sequencing these regions.

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Acknowledgments

This work was supported by the National Research Foundation of Korea (NRF) Grant Fund (MEST 2012-044048 and MEST 2010-0029131) and the conservation and restoration of rare and endemic plants research programme fund of the Korea National Arboretum of the Korea Forest Service (KNA1-2-10, 10-1). The authors thank Dr. Tomohisa Yugawa (Tsukuba Botanical Garden, National Museum of Nature and Science, Tokyo, Japan), Dr. Yung-I Lee (National Museum of Natural Science, Taiwan), and Dr. Sung Won Son (Korea National Arboretum) for providing the plant materials.

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  1. Department of Life Sciences, Gachon University, Seongnamdaero 1342, Seongnam-si, Gyeonggi-do, 461-701, South Korea

    Jung Sung Kim, Hyoung Tae Kim & Joo-Hwan Kim

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  1. Jung Sung Kim
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Correspondence to Joo-Hwan Kim.

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Jung Sung Kim and Hyoung Tae Kim contributed equally to this study.

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Supplementary Fig. 1

An example of heteroplasmy found in the petN-psbM region. Three clones were generated from the same PCR products using the same primer set with the same length. However, 1–2-bp deletions of poly(A) or (T), a 1-bp deletion, a larger deletion of 19 bp, and a tandem repeat were found among the clones. (JPEG 825 kb)

Supplementary Fig. 2

Pseudogenisation of matK in the plastid genome of Korean, Japanese, and Chinese C. japonicum (with asterisk), which was confirmed in this study, caused by a 1-bp deletion of poly(A). (JPEG 1285 kb)

Supplementary Fig. 3

Examples of AT-rich regions in the plastid genome of C. japonicum. (A) AT-rich regions between clpP and psbB. (B) AT-rich regions between petN and psbM. (JPEG 2287 kb)

Supplementary Fig. 4

Comparison of the complete plastid genomes among eight representative orchids. (JPEG 1015 kb)

Supplementary Table 1

Information on the samples used for the microsatellite study (DOCX 17 kb)

Supplementary Table 2

Comparison of SI composition among the orchid plastid genomes (DOCX 23 kb)

Supplementary Table 3

Comparison of the proportion of AT between slipper orchid and 345 angiosperm plastid genomes (XLSX 72 kb)

Supplementary Table 4

Comparison of gene losses in the orchid plastid genomes (XLSX 17 kb)

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Kim, J.S., Kim, H.T. & Kim, JH. The Largest Plastid Genome of Monocots: a Novel Genome Type Containing AT Residue Repeats in the Slipper Orchid Cypripedium japonicum . Plant Mol Biol Rep 33, 1210–1220 (2015). https://doi.org/10.1007/s11105-014-0833-y

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